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I recently expressed some discouragement about the capabilities of blogs for critiquing scientific papers. I still have those reservations, but here is a data point that leans the other way:

Doolittle and Zhaxybayeva first summarize Pallen & Matzke (2006):

Last October, Pallen and Matzke [1] summarized in a review much of the relevant knowledge. Bacterial flagella are, in fact, diverse in composition (and quite distinct from archaeal analogs), but concerning eight axial bacterial proteins these authors inferred that “the flagellar rod-hook-filament complex has clearly evolved by multiple rounds of gene duplication and subsequent diversification, starting from just two proteins (a proto-flagellin and a proto-rod/hook protein)”. There are also many homology relationships to non-flagellar proteins. As Matzke puts it (personal communication): “of 42 so-called standard flagellar proteins in Escherichia coli/Salmonella, only 20 are universally required/detectable in all flagella, only 15 have no known homologs, and only two are both universally required and have no homologs.” So the stage seems set for a more detailed accounting of the events, intermediate functions and selective pressures giving rise to these amazing structures.

Then we get to Liu & Ochman (2007):

A giant step in that direction has now been claimed by Liu and Ochman [2]. The paper quickly attracted (favorable) comment in ScienceNOW [3] and set off a firestorm of commentary (pro and con) in the evolutionary blogosphere. In ScienceNOW, Michael Lynch is quoted as saying “Complexity builds out of simplicity, and this [the Liu and Ochman paper] is a well-documented argument for how that can happen.” Maybe so, but there are some caveats we evolutionists should consider before hailing Liu and Ochman [2] as our next champions in the war against unreason. It is important that we scrutinize their arguments with special care, because they are likely to be under contention at the next trial.

This is a particularly important point – for better or worse, and as ridiculous as it seems outside of American battles over creationism, flagellum evolution has basically become a widely-followed exemplar for comparing (1) evolutionary reconstruction of the historical origins of complex structures, with (2) creationist claims that the natural origin of such structures is impossible. And it will almost certainly be featured if there is another creationism trial in the future – for example, the Discovery Institute’s new textbook, the one with the dastardly title Explore Evolution: The Arguments For and Against Neo-Darwinism (take a good look their website: make no mistake, this will be the future of creationism) doesn’t officially mention intelligent design. But it does devote a chapter to the bacterial flagellum and reiterating the usual half-baked ID arguments about it. (And yes, Explore Evolution copies the exact same Minnich-derived mistake that was pointed out in Pallen & Matzke (2006), and which the ID guys shamefully will not admit to.)

Hey, well at least the flagellum is different from the vertebrate eye, which has pretty much been done to death in evolution popularizations in my humble opinion.

Doolittle and Zhaxybayeva continue by reviewing the criticisms of Liu & Ochman’s proposal:

Liu and Ochman [2] present two conclusions about the evolutionary histories of the 24 ‘core’ flagellar genes in Bacteria that they consider ancestral for all flagellated bacteria. First, they assert that all 24 (not just eight) are homologous to each other, deriving from a single ancestor through successive duplications and diversifications, a sequence of events they reconstruct with phylogenetic analyses. Second, they argue that lateral gene transfer (LGT) has played only a minor role in the evolution of these 24 genes, that with only two exceptions “each of the genes has followed a common history in bacteria since they originated” (presumably at an early time, prior to the divergence of the major bacterial lineages).

The evidence presented for the first claim is the apparently significant BLAST scores between many individual flagellar genes, collectively uniting them all. This “single ancestor for all core flagellar proteins” hypothesis is, however, heavily criticized on the Panda’s Thumb weblog (http://www.pandasthumb.org/) by Matzke, [see note* - NM] who suggests that faulty setting of BLAST defaults has misled Liu and Ochman [2], and that homologies beyond those among axial proteins already noted are misinterpreted. Equally problematic, we think, is their conclusion that “proteins forming the flagellum, the rod, hook and filament proteins, originated in an order that mirrors the ‘inside-out’ flagellar assembly process”. Common sense might suggest such a scenario, but only rooted trees, which Liu and Ochman [2] do not provide, can prove it.

Doolittle and Zhaxybayeva then move on to another issue with the analysis in the Liu & Ochman paper, namely the paper’s conclusion that Lateral Gene Transfer (LGT) was relatively rare, effecting only four of the flagellar systems in the analysis. D&Z’s main point is that L&O’s trees of individual genes often have insufficient signal to statistically distinguish “LGT” from no “LGT”, and that the real conclusion in such situations should be “can’t tell with these data.” This issue is much closer to the cutting edge I think. It is a fairly common practice to stick together a number of genes to get more signal and higher-resolution phylogenies. I might be wrong, but I don’t think there is a standard test that is routinely applied to formally assess the statistical probability of LGT having occurred in each of the genes (if not, I might have a graduate research project right there). Presumably if LGT was a truly massive confounding issue, then stringing together genes would rarely or never produce phylogenies with improved resolution and statistical confidence, which I doubt many people would claim.

In the case of flagella, we have some background information that gives some reasons why many flagellar genes might be inherited together rather than being subject to a tremendous amount of individual LGT, e.g.: (1) the proteins form a coadapted complex and presumably the native protein is usually better adapted to function within the complex than a foreign replacement would be, (2) in the known cases of flagellar LGT (at least one of Liu & Ochman’s identified cases was known from earlier work), it is the whole flagellar system that gets laterally transferred (except for proteins like FliC – flagellin – which are highly variable and often exist in multiple divergent copies even in single genomes and single flagella, (3) LGT of both individual flagellar genes and whole flagellar complexes would presumably be easier between bacteria that are more closely related, because the flagellum has to interact with the inner membrane, cell wall, and outer membrane, and the latter two especially can vary dramatically between bacterial phyla, as can the cell’s system for regulating the construction of flagella, (4) if #3 is at least somewhat true, LGT will be both harder to detect and less relevant anyway for resolving the most interesting deep branches (most interesting if you are interested in flagellar origins, at least).

On the other hand, Doolittle is pretty keen on LGT – it’s his thing – and might not be otherwhelmed with general qualitative arguments. If, say, he was one of your reviewers on a paper, how would you convince him? One method might be to look at all of the flagellar genes under consideration and see if they are found near to each other in the bacterial genome. In some bacteria (particularly some convenient model organisms), many of the flagellar genes are grouped together in a unit, implying that they constitute a tightly-linked functional group, but often this is not the case. (Liu and Ochman were kind enough to send me some forthcoming work that bears on exactly this point; I won’t discuss it until published but it is clear it will be much less controversial than the PNAS paper.) It is also possible that one might measure generic LGT probability for particular genes by looking only at recent phylogenetic events where you have a high-resolution gene phylogeny, and use that to at least eliminate the genes that are highly subject to LGT. Anyhow, it’s a tough question and I’m not sure there will be an easy solution.

Notes

*Note: In all honesty this bit of it was worked out in discussions with Ian Musgrave and Doug Theobald, who deserve equal or more credit than me. I just blogged it, although I had already been beating the drums based on more general problems. And Liu & Ochman forthrightly volunteered the filters correction to correspondents.

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Congratulations. I am glad to see that this topic is finally getting some of the attention that it deserves. I believe that I did recommend both phylogenetic reconstruction and gene mapping previously as possibly useful approaches. Hopefully continued progress on these issues will serve as a prime example of the scientific process in action. Anyway, it sure beats “don’t know how this could possibly happen”.

As far as lateral gene transfer is concerned, this issue could be difficult to address. Hopefully comparative sequence data will help. It does seem unlikely that this would occur frequently enough to confuse the results significantly, but proving that statistically could be very difficult.

It is also good to see that the discussion here has been noticed and may play some useful role in the process. I must admit that I had my doubts about how appropriate some of the discussion here had been. It is good to see that your hard work on science and on communicating science have both been recognized.

If evolution is completely true all down the line, then why aren’t there creatures that are currently representing the middle stages of the transformations from one species to another at the mammalian level?

To be honest, though, I have seen some really inner city people, when I visited my friend in Philly some 20 years ago, that really, really did like a lot like a monkey, or a missing link. I swear to God, but then looks CAN be deceiving.

I’m not trying to be racial or flippant. I saw it with my own eyes. Has anyone else had this culture-shock type of experience (for lack of a french word)? I know what I am talking about is very politically incorrect; but please, can someone expound on this?

“If evolution is completely true all down the line, then why aren’t there creatures that are currently representing the middle stages of the transformations from one species to another at the mammalian level?”

This is way off topic, so I don’t know if the moderator will allow this discussion, but as long as you asked. You can find many examples of mammalian transitional forms, complete with references at the following web site:

talkorigins.org/faq/faq-transitional/part2a.html

You can also find many other examples of transitional forms in the other sections at this web site.

Nice summation, the 3 issues: The homology, order of appearance, and the issue of LGT all will surely be hammered by the ID crowd. I think Dolittle is sounding a clear warning bell that those who use experimental systems that are the favorites of the ID community. Researchers can expect to have their work scrutinized by these individuals for any tidbits they can utilize for their benefit which in turn requires closer attention to methodology and the resulting conclusions.

In a broader sense exaggerated claims for relationships between proteins from different organisms when not put into the proper context of a hypothesis only leads to further confusion in the literature.

Is a little blog-whoring allowed? Since Doolittle’s name has come up: last night I saw Paul Nelson trying to abuse Doolittle’s reputation and views on TV. Fortunately, Jerry Coyne was there to call him on it.

ABSTRACT: BACKGROUND: As bacteria, motile archaeal species swim by means of rotating flagellum structures driven by a proton gradient force. Interestingly, experimental data have shown that the archaeal flagellum is non-homologous to the bacterial flagellum either in terms of overall structure, components and assembly. The growing number of complete archaeal genomes now permits to investigate the evolution of this unique motility system. RESULTS: We report here an exhaustive phylogenomic analysis of the components of the archaeal flagellum. In all complete archaeal genomes, the genes coding for flagellum components are co-localized in one or two well-conserved genomic clusters showing two different types of organizations. Despite their small size, these genes harbor a good phylogenetic signal that allows reconstruction of their evolutionary histories. These support a history of mainly vertical inheritance for the components of this unique motility system, and an interesting possible ancient horizontal gene transfer event (HGT) of a whole flagellum-coding gene cluster between Euryarchaeota and Crenarchaeota. CONCLUSIONS: Our study is one of the few exhaustive phylogenomics analyses of a non-informational cell machinery from the third domain of life. We propose an evolutionary scenario for the evolution of the components of the archaeal flagellum. Moreover, we show that the components of the archaeal flagellar system have not been frequently transferred among archaeal species, indicating that gene fixation following HGT can also be rare for genes encoding components of large macromolecular complexes with a structural role.

Although I’m a big believer in free expression, this is a moderated site, and I think you should be banned for that blatant ethnic slur. I don’t see any reason why obscenity, threats, or ethnic bigotry should be tolerated here.

Since you apparently haven’t been yet (opening a window of opportunity for a serious apology), here’s the answer to your “question”.

why aren’t there creatures that are currently representing the middle stages of the transformations from one species to another at the mammalian level?

This very site featured a prolonged discussion of mouse speciation on Madeira. I believe you were part of it, but I may misremember.

If all that mouse chromosome stuff is too complicated, how about horses, donkeys, and zebra species? (I shouldn’t assume too much. Zebras are horse-like animals that live mainly in Africa. http://en.wikipedia.org/wiki/Zebra.)

Zebra species can cross with each other and with horses and donkeys to some degree. The offspring may or may not be fertile (it’s actually quite complicated). Horses and donkeys will happily mate, but the offspring, mules, are infertile.

So Nick, does this article change your publication plans?
I don’t see why it should. I think that you must have additional publishable material, and adding this new paper (how did they pass review so fast?) will only make your position better.

Oddly, I have some tiny smattering of experience with wallabies (I bet that’s the only time someone on Earth uses that particular sentence today), but I simply blanked on the fact that platapoids used different plumbing.

Somewhere deep, I actually knew that, but apparently I keep monotreme biology too deep to get to on short notice (much like the junk at the bottom of all my closets)

Maybe this will pass you by, but here goes. The dogmatic view of the world isn’t useful when dealing with empirical methods. Among other things we have discovered is that ‘Truth’ is false and ‘truth’ is uncertain.

Facts are verifiable so in that sense they are “true”. Perhaps the objects that gives observable facts are real. Or not. Who cares? (Except for one or two philosophers. And, I must confess, I do at times. Or not. :-)

Theories are testable, but since they are provisional they aren’t true, they are correct. OTOH, a formal theory can give tell you what is “true” and “false” within that theory.

Evolution is observable (“common descent”) so it is a fact. I expect biological theories to be tested as in any science, so correct as far as the tests goes. But we don’t expect theories in any science to be ‘completely correct’ or even complete.

Chris Torvik wrote:

I have seen

Since speciation is about inter- and intrafertility (for species described by the “biological species concept”), looks and 2 $ will give you a cup of coffee.

Horses and donkeys will happily mate, but the offspring, mules, are infertile.

Female horses crossed with male donkeys will become mules that are almost all sterile, however, a male horse with a female donkey will produce a Hinny, which are more likely to be fertile than are mules. Just thought I’d add an addendum to an otherwise good comment.http://en.wikipedia.org/wiki/Hinny

I agree that seeing PT referenced this way is a point in favor of blogging as a useful part of scientific discourse. It would be better, however, if the reference was more specific to particular posts. That would allow a differentiation between blogging as hyperventilating reaction (as in the first two posts on this topic) and blogging as swift collaboration and circulation of results (as in the third and subsequent posts).

Addendum to my addendum, I re-read the Hinny page, and it doesn’t seem to indicate that Hinnies are more likely to be fertile than Mules, I guess they are so rare already that this is hard to measure. I wonder where I read that factoid?

Now this is what I was waiting for, since I knew that this paper was in the pipeline. This paper is an excellent response on the issue and pretty much how I would have liked to have seen it handled from the outset. Good commentary here Nick. I am slightly embarrassed to say I don’t know nearly as much about LGT as I should given the people I am surrounded with on a daily basis. (I’m in the lab next door to Dr. Doolittle’s for those of you who may be wondering)

I think Nick you are right in saying there isn’t one definitive test for LGT but there are a lot of commonly used methods that people do use. There is also a rather large amount of work being done surrounding the methodology behind gene concatenation, super matrices, etc in terms of reconstructing large multi-gene phylogenies. I’m privileged to be working with some of the people doing excellent work on that area. Of course my own work centers around phylogenetic based methods for making predictions about protein structure and functional regions.

It does seem unlikely that this would occur frequently enough to confuse the results significantly, but proving that statistically could be very difficult.

Maybe it is just because of the research group I have been exposed to, but I happen to believe that it is quite rampant. Microbes, in their natural environment, are swapping genetic material around like crazy. You start looking at things like Gene cassettes, pathogenecity islands, plenty of genes involved in various metabolic pathways, etc. They get transfered quite frequently and without proper modeling and careful selection of genes it can prove to be a real problem in phylogenetic reconstruction. But then of course how big of a problem it is depends on how you approach the issue, the techniques you use, and maybe more importantly the question you are asking.

Yes, because the difference in paternal and maternal species in crossbreeding seems to matter. At least according to my own factoid, which I believe I picked up in discussions on crossbreeding in cats, which seems to happen quite often. But I’m too lazy to check either factoid right now.

If evolution is completely true all down the line, then why aren’t there creatures that are currently representing the middle stages of the transformations from one species to another at the mammalian level?

I gather however that you aren’t interested in the fossil record, but in current species.

There are two possible answers to the question. One is that the question is a bit confused; you can’t identify a middle-point between A and B if B is unknown because it doesn’t exist. However if you want to know about species that are currently in the process of splitting into two or more different species, then the answer is that there are many, many examples. Mammals aren’t my area, but here are a few of the many bird examples I could give: Pied Wagtail Motacilla (alba) yarrelli, the Yellow Wagtail complex Motacilla flava, Yellow-legged/Pontic gull Larus (cachinnans) michahellis, Redpoll Carduelis (flammea) cabaret.

To be clear: I think I understand the process by which the colour of an animal develops to give it a favourable chance of surviving in its given environment. What I don’t understand is the process that would result in a creature that changes a key aspect of its physiology regularly throughout it’s lifetime.

The best I can come up with so far is that the adaptation is a chemical one, where a change in, say, temperature, causes some substance to be releasd into the body, thereby altering the pigmentation and triggering a physical change in appearance. but I’ve been unable, so far, to find any reference to the process in question.

Yet more evidence of science (and scientists) at work. I've made two posts about the PNAS paper by Renyi Liu and Howard Ochman claiming that “core components of the bacterial flagellum originated through the successive duplication and modificatio...